PDE3_DICDI
ID PDE3_DICDI Reviewed; 466 AA.
AC B0G0Y8; Q8I6Y6;
DT 10-FEB-2009, integrated into UniProtKB/Swiss-Prot.
DT 18-MAR-2008, sequence version 1.
DT 03-AUG-2022, entry version 73.
DE RecName: Full=cGMP-specific 3',5'-cGMP phosphodiesterase 3;
DE EC=3.1.4.35 {ECO:0000269|PubMed:11171061};
DE AltName: Full=Phosphodiesterase 3;
DE Short=DdPDE3 {ECO:0000303|PubMed:11171061};
GN Name=pde3; ORFNames=DDB_G0268634;
OS Dictyostelium discoideum (Slime mold).
OC Eukaryota; Amoebozoa; Evosea; Eumycetozoa; Dictyostelia; Dictyosteliales;
OC Dictyosteliaceae; Dictyostelium.
OX NCBI_TaxID=44689;
RN [1]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA], FUNCTION, CATALYTIC ACTIVITY,
RP BIOPHYSICOCHEMICAL PROPERTIES, CHARACTERIZATION, DEVELOPMENTAL STAGE, AND
RP DISRUPTION PHENOTYPE.
RX PubMed=11171061; DOI=10.1042/0264-6021:3530635;
RA Kuwayama H., Snippe H., Derks M., Roelofs J., Van Haastert P.J.M.;
RT "Identification and characterization of DdPDE3, a cGMP-selective
RT phosphodiesterase from Dictyostelium.";
RL Biochem. J. 353:635-644(2001).
RN [2]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=AX4;
RX PubMed=15875012; DOI=10.1038/nature03481;
RA Eichinger L., Pachebat J.A., Gloeckner G., Rajandream M.A., Sucgang R.,
RA Berriman M., Song J., Olsen R., Szafranski K., Xu Q., Tunggal B.,
RA Kummerfeld S., Madera M., Konfortov B.A., Rivero F., Bankier A.T.,
RA Lehmann R., Hamlin N., Davies R., Gaudet P., Fey P., Pilcher K., Chen G.,
RA Saunders D., Sodergren E.J., Davis P., Kerhornou A., Nie X., Hall N.,
RA Anjard C., Hemphill L., Bason N., Farbrother P., Desany B., Just E.,
RA Morio T., Rost R., Churcher C.M., Cooper J., Haydock S., van Driessche N.,
RA Cronin A., Goodhead I., Muzny D.M., Mourier T., Pain A., Lu M., Harper D.,
RA Lindsay R., Hauser H., James K.D., Quiles M., Madan Babu M., Saito T.,
RA Buchrieser C., Wardroper A., Felder M., Thangavelu M., Johnson D.,
RA Knights A., Loulseged H., Mungall K.L., Oliver K., Price C., Quail M.A.,
RA Urushihara H., Hernandez J., Rabbinowitsch E., Steffen D., Sanders M.,
RA Ma J., Kohara Y., Sharp S., Simmonds M.N., Spiegler S., Tivey A.,
RA Sugano S., White B., Walker D., Woodward J.R., Winckler T., Tanaka Y.,
RA Shaulsky G., Schleicher M., Weinstock G.M., Rosenthal A., Cox E.C.,
RA Chisholm R.L., Gibbs R.A., Loomis W.F., Platzer M., Kay R.R.,
RA Williams J.G., Dear P.H., Noegel A.A., Barrell B.G., Kuspa A.;
RT "The genome of the social amoeba Dictyostelium discoideum.";
RL Nature 435:43-57(2005).
RN [3]
RP FUNCTION, AND SUBCELLULAR LOCATION.
RX PubMed=12429832; DOI=10.1091/mbc.e02-05-0302;
RA Bosgraaf L., Russcher H., Snippe H., Bader S., Wind J.,
RA Van Haastert P.J.M.;
RT "Identification and characterization of two unusual cGMP-stimulated
RT phosphodiesterases in dictyostelium.";
RL Mol. Biol. Cell 13:3878-3889(2002).
RN [4]
RP IDENTIFICATION.
RX PubMed=16234315; DOI=10.1093/bioinformatics/bti726;
RA Booth E.O., Van Driessche N., Zhuchenko O., Kuspa A., Shaulsky G.;
RT "Microarray phenotyping in Dictyostelium reveals a regulon of chemotaxis
RT genes.";
RL Bioinformatics 21:4371-4377(2005).
RN [5]
RP SUBCELLULAR LOCATION.
RX PubMed=17040207; DOI=10.1042/bj20061153;
RA Bader S., Kortholt A., Van Haastert P.J.M.;
RT "Seven Dictyostelium discoideum phosphodiesterases degrade three pools of
RT cAMP and cGMP.";
RL Biochem. J. 402:153-161(2007).
CC -!- FUNCTION: Phosphodiesterase specific for cGMP, which is not activated
CC by cGMP. Involved in the degradation of intracellular cGMP.
CC {ECO:0000269|PubMed:11171061, ECO:0000269|PubMed:12429832}.
CC -!- CATALYTIC ACTIVITY:
CC Reaction=3',5'-cyclic GMP + H2O = GMP + H(+); Xref=Rhea:RHEA:16957,
CC ChEBI:CHEBI:15377, ChEBI:CHEBI:15378, ChEBI:CHEBI:57746,
CC ChEBI:CHEBI:58115; EC=3.1.4.35;
CC Evidence={ECO:0000269|PubMed:11171061};
CC PhysiologicalDirection=left-to-right; Xref=Rhea:RHEA:16958;
CC Evidence={ECO:0000269|PubMed:11171061};
CC -!- COFACTOR:
CC Name=a divalent metal cation; Xref=ChEBI:CHEBI:60240;
CC Evidence={ECO:0000250};
CC Note=Binds 2 divalent metal cations per subunit. Site 1 may
CC preferentially bind zinc ions, while site 2 has a preference for
CC magnesium and/or manganese ions. {ECO:0000250};
CC -!- ACTIVITY REGULATION: Inhibited by 3-isobutyl-1-methylxanthine (IBMX).
CC -!- BIOPHYSICOCHEMICAL PROPERTIES:
CC Kinetic parameters:
CC KM=0.22 uM for cGMP {ECO:0000269|PubMed:11171061};
CC Vmax=2 pmol/min/mg enzyme with cGMP as substrate
CC {ECO:0000269|PubMed:11171061};
CC Note=cAMP/cGMP selectivity of 0.0015. {ECO:0000269|PubMed:11171061};
CC -!- SUBCELLULAR LOCATION: Cytoplasm, cytosol {ECO:0000269|PubMed:12429832,
CC ECO:0000269|PubMed:17040207}.
CC -!- DEVELOPMENTAL STAGE: Expression is constant throughout the development.
CC {ECO:0000269|PubMed:11171061}.
CC -!- DOMAIN: Composed of a C-terminal catalytic domain containing two
CC putative divalent metal sites and an N-terminal regulatory domain.
CC -!- DISRUPTION PHENOTYPE: Shows a moderate phenotype with increased basal
CC cGMP levels, but only a small effect on cAMP-stimulated cGMP levels.
CC {ECO:0000269|PubMed:11171061}.
CC -!- SIMILARITY: Belongs to the cyclic nucleotide phosphodiesterase family.
CC {ECO:0000305}.
CC -!- SEQUENCE CAUTION:
CC Sequence=AAN78319.1; Type=Erroneous gene model prediction; Evidence={ECO:0000305};
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DR EMBL; AY162269; AAN78319.1; ALT_SEQ; Genomic_DNA.
DR EMBL; AAFI02000004; EDR41121.1; -; Genomic_DNA.
DR RefSeq; XP_001732951.1; XM_001732899.1.
DR AlphaFoldDB; B0G0Y8; -.
DR SMR; B0G0Y8; -.
DR STRING; 44689.DDB0233681; -.
DR PaxDb; B0G0Y8; -.
DR EnsemblProtists; EDR41121; EDR41121; DDB_G0268634.
DR GeneID; 8616668; -.
DR KEGG; ddi:DDB_G0268634; -.
DR dictyBase; DDB_G0268634; pde3.
DR eggNOG; KOG3689; Eukaryota.
DR HOGENOM; CLU_587163_0_0_1; -.
DR InParanoid; B0G0Y8; -.
DR OMA; WANALME; -.
DR PhylomeDB; B0G0Y8; -.
DR Reactome; R-DDI-2485179; Activation of the phototransduction cascade.
DR Reactome; R-DDI-4086398; Ca2+ pathway.
DR Reactome; R-DDI-418457; cGMP effects.
DR Reactome; R-DDI-418555; G alpha (s) signalling events.
DR Reactome; R-DDI-9013422; RHOBTB1 GTPase cycle.
DR SABIO-RK; B0G0Y8; -.
DR PRO; PR:B0G0Y8; -.
DR Proteomes; UP000002195; Chromosome 1.
DR GO; GO:0005829; C:cytosol; IEA:UniProtKB-SubCell.
DR GO; GO:0047555; F:3',5'-cyclic-GMP phosphodiesterase activity; IDA:dictyBase.
DR GO; GO:0004114; F:3',5'-cyclic-nucleotide phosphodiesterase activity; IBA:GO_Central.
DR GO; GO:0030553; F:cGMP binding; IDA:dictyBase.
DR GO; GO:0000287; F:magnesium ion binding; IDA:dictyBase.
DR GO; GO:0030145; F:manganese ion binding; IDA:dictyBase.
DR GO; GO:0019934; P:cGMP-mediated signaling; IMP:dictyBase.
DR GO; GO:0007165; P:signal transduction; IBA:GO_Central.
DR CDD; cd00077; HDc; 1.
DR Gene3D; 1.10.1300.10; -; 1.
DR InterPro; IPR003607; HD/PDEase_dom.
DR InterPro; IPR023088; PDEase.
DR InterPro; IPR002073; PDEase_catalytic_dom.
DR InterPro; IPR036971; PDEase_catalytic_dom_sf.
DR InterPro; IPR023174; PDEase_CS.
DR Pfam; PF00233; PDEase_I; 1.
DR PRINTS; PR00387; PDIESTERASE1.
DR SMART; SM00471; HDc; 1.
DR PROSITE; PS00126; PDEASE_I_1; 1.
DR PROSITE; PS51845; PDEASE_I_2; 1.
PE 1: Evidence at protein level;
KW cGMP; cGMP-binding; Cytoplasm; Hydrolase; Manganese; Metal-binding;
KW Nucleotide-binding; Reference proteome.
FT CHAIN 1..466
FT /note="cGMP-specific 3',5'-cGMP phosphodiesterase 3"
FT /id="PRO_0000363969"
FT DOMAIN 137..458
FT /note="PDEase"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU01192"
FT REGION 1..150
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 1..119
FT /note="Polar residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 135..150
FT /note="Polar residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT ACT_SITE 213
FT /note="Proton donor"
FT /evidence="ECO:0000250"
FT BINDING 217
FT /ligand="a divalent metal cation"
FT /ligand_id="ChEBI:CHEBI:60240"
FT /ligand_label="1"
FT /evidence="ECO:0000250"
FT BINDING 253
FT /ligand="a divalent metal cation"
FT /ligand_id="ChEBI:CHEBI:60240"
FT /ligand_label="1"
FT /evidence="ECO:0000250"
FT BINDING 254
FT /ligand="a divalent metal cation"
FT /ligand_id="ChEBI:CHEBI:60240"
FT /ligand_label="1"
FT /evidence="ECO:0000250"
FT BINDING 254
FT /ligand="a divalent metal cation"
FT /ligand_id="ChEBI:CHEBI:60240"
FT /ligand_label="2"
FT /evidence="ECO:0000250"
FT BINDING 364
FT /ligand="a divalent metal cation"
FT /ligand_id="ChEBI:CHEBI:60240"
FT /ligand_label="1"
FT /evidence="ECO:0000250"
SQ SEQUENCE 466 AA; 53121 MW; 1C3C557EC4D4089D CRC64;
MAPQQNIMKQ LQQMQSSPYP SSSPSSTTVS QNNDNLNHNV HSLNNSSNNN NNNNNNNNNN
NNNNNNNNNN NNNNNNNNNN NNNSINEKNK INDNNNRGNS DDGNNNNSNN NSNNNNSNNN
NRDDEEEEGD DEDNNNNNNS NNNKIRGYND NNDINDIFSI NFSSWSKSKD NLIENGVLIF
EESGLYKELN LSKSSILNFL SIVASSYRNN PFHSFNHAIA VTQTIFLILL KTNLFNILSP
IEKLSIIIAS ICHDLDHPAL SNRFQINMKS SIAVLYNNKS VLENHHLSIC LGILESKIGN
ELLSTLTVEE KKQFFRRVKI LILATDMENH FTYKKQFDDI ISTFSWDNSE HRDLLLIMFL
KSADISNELR SFDISNKWAN ALMEEFFNQS DLEKLNNLPL TPFMEREKVV LHLTQVSFIE
KFLLPSYQSL QNLLPSLEDF VQRIIENKEI WSNNGSSSST TSSSPN
